On Wed, Feb 9, 2011 at 1:08 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> I guess a lot of us have this problem: I'm storing "genome long"
> integer/doubles vectors for each position along each chromosome.
>
> I want to quickly access parts of these vectors in a manner quite
> similar/convenient/efficient to how we can quickly access the reads in
> a given region of a BAM file. I'm curios what you folks are using to
> store this type of info?
>
> Currently I just have RData objects of Rle's or XIntegers, etc. for
> each strand of each chromosome. I'll load these data files, query the
> info over the ranges I want, then junk the (usually large) vector I
> just loaded. It's not the best, but it works.
>
> In the bioinformatics world, I guess these data are best stored as
> bigWig files, yes? And AFAIK, there's no (convenient or otherwise) way
> to query bigWigs from within R/Bioc, right?
>
>
Actually, rtracklayer can query bigWigs. It's very efficient.


> Then I wonder if storing these in hdf/netcdf files isn't actually the
> way to go  ... and if so, why not go whole-hog and work on a bioc
> interface to the somehow-defined biohdf format?
>
> Any thoughts?
>
>
This is also a good idea, especially if you have data for many samples.
There's a group of us here at Genentech looking to improve upon the netcdf4
support in R. This is the first I've heard of biohdf. Sounds kind of
half-baked though.

Michael



-steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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